Startup

script/Devices/ImageStats.py

@@ -0,0 +1,137 @@
+from startup import *
+from ijutils import *
+from ch.psi.pshell.imaging.Overlays import *
+import ch.psi.pshell.imaging.Pen as Pen
+import java.awt.Color as Color
+import random
+
+
+def get_centroid(source):
+    bi = source.getImage()    
+    if bi is None:
+        return None
+    op = show_panel(bi, "Original")
+    ip = load_image(bi)  
+    plot(get_histogram(ip), title = "Histogram")  
+    grayscale(ip)    
+    invert(ip)
+    gaussian_blur(ip)    
+    auto_threshold(ip)
+    
+    #binary_erode(ip)        
+    show_panel(ip.getBufferedImage(), "Image")
+    (results,output_img)=analyse_particles(ip, 2000,20000, exclude_edges=False, print_table=True)    
+    op.clearOverlays()
+    show_panel(output_img.getBufferedImage(), "Outlines")
+    if results.size()>0:        
+        centroid  = (results.getValue("XM",0), results.getValue("YM",0))
+        ov = Crosshairs(Pen(Color.ORANGE),  java.awt.Point(int(centroid[0]),int(centroid[1])), java.awt.Dimension(15,15))
+        op.addOverlay(ov)
+        return centroid    
+              
+
+
+
+import ch.psi.pshell.imaging.Filter as Filter
+
+class SimulatedSource(Filter):
+    def process(self, img, data):      
+        self.img=img  
+        if img is None: 
+            return None 
+        ip = load_image(img)         
+        pad_h = int((random.random()-0.5) * 500)
+        pad_v = int((random.random()-0.5) * 500)
+        #print "Pad = " , (pad_h, pad_v)
+        ip = pad_image(ip, -pad_h, pad_h, pad_v, -pad_v, fill_color = Color.BLACK)
+        return ip.getBufferedImage() 
+        #return img
+        
+    def waitNext(self, timeout):
+        self.pushImage(self.process(self.img, None))
+        
+        
+       
+class ImageStats(DeviceBase):
+    def __init__(self, name, source):
+        DeviceBase.__init__(self, name)
+        self.source = source
+        self.com_x_samples, self.com_y_samples = [], []
+        class ComX(Readable):
+            def read(self):     
+                if len(self.image_stats.com_x_samples)==0: return None
+                return mean(self.image_stats.com_x_samples)
+        self.com_x_mean = ComX(); self.com_x_mean.image_stats = self
+        class ComY(Readable):
+            def read(self):     
+                if len(self.image_stats.com_y_samples)==0: return None
+                return mean(self.image_stats.com_y_samples)
+        self.com_y_mean = ComY(); self.com_y_mean.image_stats = self
+        class ComXVar(Readable):
+            def read(self):     
+                if len(self.image_stats.com_x_samples)==0: return None
+                return stdev(self.image_stats.com_x_samples)
+        self.com_x_stdev = ComXVar(); self.com_x_stdev.image_stats = self
+        class ComXVar(Readable):
+            def read(self):     
+                if len(self.image_stats.com_y_samples)==0: return None
+                return stdev(self.image_stats.com_y_samples)
+        self.com_y_stdev = ComXVar(); self.com_y_stdev.image_stats = self
+        set_device_alias(self.com_x_mean, name + " com x mean")
+        set_device_alias(self.com_y_mean, name + " com y mean")
+        set_device_alias(self.com_x_stdev, name + " com x stdev")
+        set_device_alias(self.com_y_stdev, name + " com y stdev")
+        self.bg_en = False
+        self.num_images = 1
+        self.initialize()        
+    
+    
+    def doUpdate(self):        
+        self.com_x_samples, self.com_y_samples = [], []
+        for i in range(self.num_images):
+            if type(self.source) is not  ch.psi.pshell.imaging.FileSource:                                
+                self.source.waitNext(3000)                
+            centroid = get_centroid(self.source)            
+            print "cent ", centroid            
+            if centroid is not None:
+                self.com_x_samples.append(centroid[0])
+                self.com_y_samples.append(centroid[1])
+
+    def setNumberOfImages(self, value):
+        self.num_images = value
+
+    def enableBackground(self, value):
+        self.bg_en = value
+        
+    def captureBackground(self, images):               
+        self.doInitialize()
+    
+    def doClose(self):        
+        pass    
+
+    def start(self):
+        pass
+
+    def stop(self):
+        pass
+        
+
+def get_simulated_source(img):
+    simulated_source = SimulatedSource()           
+    simulated_source.img=None
+    simulated_source.initialize()
+    img.addListener(simulated_source)
+    show_panel(simulated_source)
+    return simulated_source
+
+if __name__ == "__builtin__":
+    simulated_source = get_simulated_source(image)           
+    print get_centroid(simulated_source)        
+    
+    add_device(ImageStats("image_stats", simulated_source), True)
+    image_stats.enableBackground(False)    
+    for i in range (10):        
+        image_stats.update()        
+        print image_stats.take(), image_stats.com_x_mean.read(), image_stats.com_y_mean.read() 
+        time.sleep(1)
+